Hepatitis B Genetic Evolution from Stone Age Uncovered

Understanding the molecular origins of infectious diseases such as hepatitis B can provide valuable insight as to how viral pathogens spread through human populations and the mutations that lead to increased virulence. Now, an international team of scientists led by investigators at the Max Planck Institute for the Science of Human History and the University of Kiel has been able to successfully reconstruct the genomes of hepatitis B isolated from Stone Age and Medieval skeletal remains. Findings from the new study—published recently in eLife, in an article entitled “Neolithic and Medieval Virus Genomes Reveal Complex Evolution of Hepatitis B”—indicates that hepatitis B was circulating in Europe at least 7000 years ago.

The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, affecting over 250 million people worldwide. However, its origin and evolutionary history have been unclear. Studying the evolution and history of the virus has to date been especially difficult because until now viral DNA had not been successfully recovered from prehistoric samples. The researchers in the current study not only recovered ancient viral DNA from skeletons but also reconstructed the genomes of three strains of HBV. While the ancient virus is similar to its modern counterparts, the strains represent a distinct lineage that has likely gone extinct and is most closely related to chimpanzee and gorilla viruses.

Skeletal remains of HBV-positive individual from the Stone Age site of Karsdorf, Germany. The individual was a male with an age at death of around 25–30 years. [Nicole Nicklisch/???State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory]

“We report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany,” the authors wrote. “We reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results show that HBV circulates in the European population for at least 7000 years.”

The researchers analyzed samples from the teeth of 53 skeletons dated from around 5000 BC to 1200 AD. The researchers screened all samples for viral pathogens and detected ancient HBV in three of the individuals. Full HBV genomes were recovered from these samples, two of which were from the Neolithic period, dating to about 7000 and 5000 years ago, and one from the medieval period. The Neolithic genomes represent the by far oldest virus genomes reconstructed to date.

“The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African nonhuman primates,” the authors remarked. “These ancient virus forms appear to represent distinct lineages that have no close relatives today and possibly went extinct.”

Geographic location of the samples from which ancient HBV genomes were recovered. Icons indicate the sample material (tooth or mummy). HBV genomes obtained in this study are indicated by black frames. [Krause-Kyora et al., eLife 2018]

Interestingly, the two Neolithic genomes, although recovered from individuals that lived 2000 years apart, were relatively similar to each other in comparison with modern strains and were, in fact, more closely related to modern strains of HBV found in chimpanzees and gorillas. In contrast, the Medieval HBV genome is more similar to modern strains but still represents a separate lineage. This is the case even when it is compared to two previously published HBV genomes recovered from mummies dating to the 16th century. The HBV strains found in these mummies are closely related to modern strains, suggesting a surprising lack of change in the virus over the last 500 years. These findings point to a complicated history for the virus, which may have involved multiple cross-species transmission events.

“Taken together, our results demonstrate that HBV already existed in Europeans 7000 years ago and that its genomic structure closely resembled that of modern hepatitis B viruses, despite the differences observed,” explained lead study investigator Ben Krause-Kyora, Ph.D., professor at the Max Planck Institute for the Science of Human History and Kiel University. “More ancient precursors, intermediates, and modern strains of both human and nonhuman primate HBV strains need to be sequenced to disentangle the complex evolution of this virus.”

Senior study investigator Johannes Krause, Ph.D., professor, and director of the department of archaeogenetics at the Max Planck Institute for the Science of Human History, emphasized the most important implication of the study. “Our results reveal the great potential of ancient DNA from human skeletons to allow us to study the evolution of blood-borne viruses. Previously, there was doubt as to whether we would ever be able to study these diseases directly in the past. We now have a powerful tool to explore the deep evolutionary history of viral diseases.”